Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH)

Juan I Montoya-Burgos,Ilham Bahechar,Aurélia Foulon

doi:10.1186/1471-2164-11-126

Abstract

BackgroundFast evolving genes are targets of an increasing panel of biological studies, from cancer research to population genetics and species specific adaptations. Yet, their identification and isolation are still laborious, particularly for non-model organisms. We developed a method, named the Inter-Specific Selective Hybridization (ISSH) method, for generating cDNA libraries enriched in fast evolving genes. It utilizes transcripts of homologous tissues of distinct yet related species. Experimental hybridization conditions are monitored in order to discard transcripts that do not find their homologous counterparts in the two species sets as well as transcripts that display a strong complementarity between the two species. Only heteroduplexes that disanneal at low stringency are used for constructing the resulting cDNA library.ResultsWe demonstrate the efficiency of the ISSH method by generating a brain cDNA library enriched in fast evolving transcripts of a non-model catfish species as well as a control, non-enriched library. Our results indicate that the enriched library contains effectively more fast evolving sequences than the control library. Gene annotation analyses also indicate enrichment in genes with low expression levels and non-ubiquitously expressed genes, both categories encompassing the majority of fast evolving genes. Furthermore, most of the identified transcripts show higher sequence divergence between two closely related catfish species as compared to recognized fast evolving DNA markers.ConclusionsThe ISSH method offers a simple, inexpensive and efficient way to screen the transcriptome for isolating fast evolving genes. This method opens new opportunities in the investigation of biological mechanisms that include fast evolving genes, such as the evolution of lineage specific processes and traits responsible for species adaptation to their environment.

Highlights

Fast evolving genes are targets of an increasing panel of biological studies, from cancer research to population genetics and species specific adaptations
The property of evolving fast implies that such transcripts will disanneal at low stringencies from the heteroduplexes formed by homologous complementary sequences of the two species
We have shown that the overall sequence divergence was significantly increased in the enriched library as compared to the control when blasting these libraries against the zebrafish genome or against our Hypostomus catfish EST library

Summary

Introduction

Fast evolving genes are targets of an increasing panel of biological studies, from cancer research to population genetics and species specific adaptations Their identification and isolation are still laborious, for non-model organisms. We developed a method, named the Inter-Specific Selective Hybridization (ISSH) method, for generating cDNA libraries enriched in fast evolving genes It utilizes transcripts of homologous tissues of distinct yet related species. Theoretical approaches suggest that adaptation genes should be fast evolving so that selection could have a substrate on which to act [16] Speciation genes, those that are directly or indirectly involved in the establishment of the genetic barrier between closely related species, consistently displayed high divergence rates [11]. The increasing interest in biological mechanisms driven by fast evolving genes appeals to the development of a more efficient and cost effective method for the isolation of such genes across closely related species and which would not imply the prior knowledge of genetic or genomic information

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Discussion

Conclusion